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Items: 1 to 20 of 405


Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data.

Gupta R, Wikramasinghe P, Bhattacharyya A, Perez FA, Pal S, Davuluri RV.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S65. doi: 10.1186/1471-2105-11-S1-S65.


Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.

Sun H, Wu J, Wickramasinghe P, Pal S, Gupta R, Bhattacharyya A, Agosto-Perez FJ, Showe LC, Huang TH, Davuluri RV.

Nucleic Acids Res. 2011 Jan;39(1):190-201. doi: 10.1093/nar/gkq775. Epub 2010 Sep 14.


Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.

Pal S, Gupta R, Davuluri RV.

Methods Mol Biol. 2014;1176:1-9. doi: 10.1007/978-1-4939-0992-6_1.


Integrative genome-wide chromatin signature analysis using finite mixture models.

Taslim C, Lin S, Huang K, Huang TH.

BMC Genomics. 2012;13 Suppl 6:S3. doi: 10.1186/1471-2164-13-S6-S3. Epub 2012 Oct 26.


MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.

Gupta R, Bhattacharyya A, Agosto-Perez FJ, Wickramasinghe P, Davuluri RV.

Nucleic Acids Res. 2011 Jan;39(Database issue):D92-7. doi: 10.1093/nar/gkq1171. Epub 2010 Nov 21.


ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.

Ho JW, Bishop E, Karchenko PV, Nègre N, White KP, Park PJ.

BMC Genomics. 2011 Feb 28;12:134. doi: 10.1186/1471-2164-12-134.


dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data.

Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keleş S.

PLoS Comput Biol. 2013;9(10):e1003246. doi: 10.1371/journal.pcbi.1003246. Epub 2013 Oct 17.


Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data.

Bedo J, Kowalczyk A.

Bioinformatics. 2011 Jun 15;27(12):1610-7. doi: 10.1093/bioinformatics/btr263. Epub 2011 May 9.


ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.

Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR.

BMC Bioinformatics. 2010 May 11;11:237. doi: 10.1186/1471-2105-11-237.


A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data.

Han Z, Tian L, Pécot T, Huang T, Machiraju R, Huang K.

BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S2. doi: 10.1186/1471-2105-13-S2-S2.


Integrative analysis of ChIP-chip and ChIP-seq dataset.

Zhu LJ.

Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8_8.


diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.

Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ.

PLoS One. 2013 Jun 10;8(6):e65598. doi: 10.1371/journal.pone.0065598. Print 2013.


Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments.

Ghosh S, Hirsch HA, Sekinger E, Struhl K, Gingeras TR.

BMC Bioinformatics. 2006 Oct 5;7:434.


Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.

Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC.

Bioinformatics. 2010 Apr 15;26(8):1000-6. doi: 10.1093/bioinformatics/btq087. Epub 2010 Mar 5.


Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

wa Maina C, Honkela A, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M.

PLoS Comput Biol. 2014 May 15;10(5):e1003598. doi: 10.1371/journal.pcbi.1003598. eCollection 2014 May.


Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37.


Differential motif enrichment analysis of paired ChIP-seq experiments.

Lesluyes T, Johnson J, Machanick P, Bailey TL.

BMC Genomics. 2014 Sep 2;15:752. doi: 10.1186/1471-2164-15-752.


Using CisGenome to analyze ChIP-chip and ChIP-seq data.

Ji H, Jiang H, Ma W, Wong WH.

Curr Protoc Bioinformatics. 2011 Mar;Chapter 2:Unit2.13. doi: 10.1002/0471250953.bi0213s33.


Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.

Chen CY, Morris Q, Mitchell JA.

BMC Genomics. 2012 Apr 26;13:152. doi: 10.1186/1471-2164-13-152.

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